Profile of microRNA in Blood Plasma of Healthy Humans

Skurnikov, M. Yu.; Makarova, J. A.; Knyazev, E N; Fomicheva, K. A.; Nyushko, K. M.; Saribekyan, E. K.; Alekseev, B. Ya.; Каприн, А. Д.

doi:10.1007/s10517-016-3235-3

Cited by 16 publications

(3 citation statements)

References 14 publications

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“…The plasma was separated according to a previously designed protocol, minimizing hemolysis and miRNA release from blood cells ( Shkurnikov et al , 2016 ). The level of hemolysis was evaluated by spectrophotometry ( Skurnikov et al , 2016 ).…”

Section: Methodsmentioning

confidence: 99%

Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer

et al. 2023

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Motivation One of the standard methods of high-throughput RNA sequencing analysis is differential expression. However, it does not detect changes in molecular regulation. In contrast to the standard differential expression analysis, differential co-expression one aims to detect pairs or clusters whose mutual expression changes between two conditions. Results We developed DCoNA (Differential Co-expression Network Analysis) – an open-source statistical tool that allows one to identify pair interactions, which correlation significantly changes between two conditions. Comparing DCoNA with the state-of-the-art analog, we showed that DCoNA is a faster, more accurate, and less memory-consuming tool. We applied DCoNA to prostate mRNA/miRNA-seq data collected from The Cancer Genome Atlas (TCGA) and compared predicted regulatory interactions of miRNA isoforms (isomiRs) and their target mRNAs between normal and cancer samples. As a result, almost all highly expressed isomiRs lost negative correlation with their targets in prostate cancer samples compared to ones without the pathology. One exception to this trend was the canonical isomiR of hsa-miR-93-5p acquiring cancer-specific targets. Further analysis showed that cancer aggressiveness simultaneously increased with the expression level of this isomiR in both TCGA primary tumor samples and 153 blood plasma samples of P. Hertsen Moscow Oncology Research Institute patients’ cohort analyzed by miRNA microarrays. Availability Source code and documentation of DCoNA are available at https://github.com/zhiyanov/DCoNA. Supplementary information Supplementary data are available at Bioinformatics online.

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Section: Methodsmentioning

confidence: 99%

Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer

et al. 2023

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“…The plasma was separated according to a previously designed protocol, minimizing hemolysis and miRNA release from blood cells [36]. The level of hemolysis was evaluated by spectrophotometry [37].…”

Section: Used Datasetsmentioning

confidence: 99%

Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer

Zhiyanov

Engibaryan

Nersisyan

et al. 2022

Preprint

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We developed DCoNA - a statistical tool that allows one to identify pair interactions, which correlation significantly changes between two conditions. Comparing DCoNA with the state-of-the-art analog, we showed that DCoNA is a faster, more accurate, and less memory-consuming tool. We applied DCoNA to prostate mRNA/miRNA-seq data collected from The Cancer Genome Atlas (TCGA) and compared predicted regulatory interactions of miRNA isoforms (isomiRs) and their target mRNAs between normal and cancer samples. As a result, almost all highly expressed isomiRs lost negative correlation with their targets in prostate cancer samples compared to ones without the pathology. One exception to this trend was the canonical isomiR of hsa-miR-93-5p acquiring cancer- specific targets. Further analysis showed that cancer aggresiveness increased with the expression of this isomiR in both TCGA primary tumor samples and 153 blood plasma samples of own patients' cohort analyzed by miRNA microarrays.

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“…Total RNA was isolated by guanidine thiocyanate–phenol–chloroform extraction [ 11 ] using the Qiagen miRNeasy Mini Kit. The RNA concentration was determined using a NanoDrop 1000 instrument [ 12 ].…”

mentioning

confidence: 99%

Chemical Induction of Trophoblast Hypoxia by Cobalt Chloride Leads to Increased Expression of DDIT3

Knyazev

Paul

Tonevitsky

2021

Dokl Biochem Biophys

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Choriocarcinoma cells BeWo b30 are used to model human placental trophoblast hypoxia using cobalt (II) chloride and hydroxyquinoline derivative (HD) as chemical inducers of hypoxia-inducible factor (HIF). In this study, it was shown that both substances activate the hypoxic pathway and the epithelial–mesenchymal transition and inhibit the pathways of cell proliferation. However, CoCl2 caused activation of the apoptosis pathway, increased the activity of effector caspases 3 and 7, and increased the expression of the unfolded protein response target DDIT3. The mTORC1 pathway was activated upon exposition to CoCl2, while HD suppressed this pathway, as it happens during real trophoblast hypoxia. Thus, effect of CoCl2 on BeWo cells can be a model of severe hypoxia with activation of apoptosis, while HD mimics moderate hypoxia.

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Profile of microRNA in Blood Plasma of Healthy Humans

Cited by 16 publications

References 14 publications

Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer

Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer

Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer

Chemical Induction of Trophoblast Hypoxia by Cobalt Chloride Leads to Increased Expression of DDIT3

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